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I am trying to load canola hybrid SNP data in GenABEL. Since I created the hybrids in silico from the Illumina genotyping files of the parents, some hybrids can contain "half deletions" (e.g. A-).According to the GenABEL manual

"Accepted allele codes: 1/2, A/B, A/T, A/G, A/C, T/G, T/C, G/C, A/-, T/-, G/-, C/-. Here, "-" stands of a deletion. Missing data can be coded as "–" or "00". Make sure that the coding for missing is "00" if you use one of the codings A/-, T/-, G/-, C/-"

I tried to code my half deletions like this (in this short testfile below):

I tried several other codings for the matrix, including T/-, -T, -/T, T0, but none of them is able to handle my "half deletions". However, it works as soon as I replace the first SNP genotype by TT, so the rest of my file seems to be correct.